[Chimera-users] molecular dynamics with phosphates: monobasic form unstable?

Geoffrey Sametz sametz at udel.edu
Sat Mar 30 11:31:53 PDT 2019

I am having my students model dipeptides where one residue is a
phosphorylated serine or threonine. Molecular dynamics with the dibasic
phosphate works fine. However, the student NMR data for their dipeptides is
acquired at low pH, so I would like them to be able to model the monobasic
form. Unfortunately, all my attempts at creating a monobasic form have
resulted in the molecule "blowing up" in MD, first by crazily shaking the
phosphate as if it wants to dislodge the proton, and then the entire
molecule until it fragments.

I have tried building these from scratch by various methods (e.g. those
listed in
) as well as using SwissSidechain and mutating residues. I have tried
exporting as a .pdb, opening in PyMOL to make sure everything looks OK,
resaving as .pdb and importing PyMOL's version.

I have also used a protein from PDB that had a TPO residue assigned, and
snipped it down to a dipeptide.For both this manner of construction, and
for building the dipeptide from scratch with SwissSidechain, Chimera
interprets SwissSidechain's TPO (pThr monobasic) and SEP (pSer monobasic)
as their dibasic forms (TPO2 and SEP2 respectively). PyMOL interprets these
structures with the correct level of protonation, however.

Is there a known issue with Chimera and treatment of [-OPO3H]-1 groups, or
have I managed to make the same error across multiple build methods?

Dr. Geoffrey Sametz
QDH 104
Department of Chemistry and Biochemistry
University of Delaware
sametz at udel.edu
(302) 831-3621
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